Align Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)
Query= TCDB::AIU41385.1 (509 letters) >FitnessBrowser__Btheta:353923 Length = 460 Score = 204 bits (518), Expect = 7e-57 Identities = 141/486 (29%), Positives = 237/486 (48%), Gaps = 48/486 (9%) Query: 17 LKKKPKRNLYAIGCAILASMTSILLGYDIGVMSGASIYIQEDLKISDVEVE--ILIGILN 74 +K K+ +Y+I ++++M +L GYD V+ GA + + I+D + + + Sbjct: 1 MKSYNKKFVYSI--CLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTMQGLAMSVAL 58 Query: 75 LYSLIGSAAAGRTSDWIGRRYTIVFAGAIFFTGALLMGFATNYAFLMVGRFVAGIGVGYA 134 L LIG+ AG +D GR+ ++ + IF + A G + +++ + RF+ GIG+G A Sbjct: 59 LGCLIGAMVAGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIA 118 Query: 135 LMIAPVYNAEVSPASSRGALTSFPEVFVNIGILLGYVANYAFSGLPI------------- 181 ++P+Y AEV+P S RG L S ++ + +GIL +AN+ + PI Sbjct: 119 SGLSPMYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAE-PIPADFTPADICASW 177 Query: 182 --NLGWRLMLGVGVFPSVILAVGVLTMPESPRWLVMQGRLGDAKHVLDKTSDSLEEAQLR 239 +GWR M FP+ + + +PESPRWL M+G+ A VL + + Sbjct: 178 NGQMGWRWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGN------- 230 Query: 240 LADIKEAAGIPEHCTEDVVQVPKHSHGEEVWKELLLHPTPPVRHILIAAVGFHFFQQMSG 299 E +Q+ + + + L L + P R +L+ V FQQ G Sbjct: 231 ------------RYAEQELQMVEQTSASKSEGGLKLLFSRPFRKVLVLGVIVAVFQQWCG 278 Query: 300 IDALVLYSPRIFRASGITDSSTLLLATVAVGFSKTIFTLIAIGFLDRVGRRPLLLTSVAG 359 + + Y+ IF+++G + +L V G + IFT +AI ++R+GRR L+L G Sbjct: 279 TNVIFNYAQEIFQSAGYS-LGDVLFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGG 337 Query: 360 MIASLLCLGTSLTIVDHEKEKMMWASVVCLTMVLAYVGFFSIGMGPIAWVYSSEIFPLKL 419 + L LGT + + +V+ + +++ +GPI WV +EIFP ++ Sbjct: 338 LAGIYLVLGTCYFF--------QVSGFFMVVLVVLAIACYAMSLGPITWVLLAEIFPNRV 389 Query: 420 RAQGCSMGTAVNRIMSGVLTMTFITLYKAITMGGTFFLYGAIATVGWVFFYTMLPETQGR 479 R + T + S LT TF L A+ GTF++Y AI G++FF LPET+G+ Sbjct: 390 RGVAMATCTFALWVGSFTLTYTFPLLNTALGSYGTFWIYSAICVFGFLFFLRALPETKGK 449 Query: 480 TLEDME 485 +LE +E Sbjct: 450 SLETLE 455 Lambda K H 0.326 0.140 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 685 Number of extensions: 35 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 509 Length of database: 460 Length adjustment: 34 Effective length of query: 475 Effective length of database: 426 Effective search space: 202350 Effective search space used: 202350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory